SUVH3_ARATH
ID SUVH3_ARATH Reviewed; 669 AA.
AC Q9C5P4; Q9SSL7;
DT 09-MAY-2003, integrated into UniProtKB/Swiss-Prot.
DT 09-MAY-2003, sequence version 2.
DT 03-AUG-2022, entry version 152.
DE RecName: Full=Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH3;
DE EC=2.1.1.367 {ECO:0000250|UniProtKB:Q5QD03};
DE AltName: Full=Histone H3-K9 methyltransferase 3;
DE Short=H3-K9-HMTase 3;
DE AltName: Full=Protein SET DOMAIN GROUP 19;
DE AltName: Full=Suppressor of variegation 3-9 homolog protein 3;
DE Short=Su(var)3-9 homolog protein 3;
GN Name=SUVH3; Synonyms=SDG19, SET19; OrderedLocusNames=At1g73100;
GN ORFNames=F3N23.30;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION, NOMENCLATURE, AND TISSUE
RP SPECIFICITY.
RX PubMed=11691919; DOI=10.1093/nar/29.21.4319;
RA Baumbusch L.O., Thorstensen T., Krauss V., Fischer A., Naumann K.,
RA Assalkhou R., Schulz I., Reuter G., Aalen R.B.;
RT "The Arabidopsis thaliana genome contains at least 29 active genes encoding
RT SET domain proteins that can be assigned to four evolutionarily conserved
RT classes.";
RL Nucleic Acids Res. 29:4319-4333(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP GENE FAMILY.
RX PubMed=16384625; DOI=10.1016/j.jplph.2005.10.015;
RA Fischer A., Hofmann I., Naumann K., Reuter G.;
RT "Heterochromatin proteins and the control of heterochromatic gene silencing
RT in Arabidopsis.";
RL J. Plant Physiol. 163:358-368(2006).
CC -!- FUNCTION: Histone methyltransferase. Methylates 'Lys-9' of histone H3.
CC H3 'Lys-9' methylation represents a specific tag for epigenetic
CC transcriptional repression. {ECO:0000250|UniProtKB:Q5QD03}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-lysyl(9)-[histone H3] + S-adenosyl-L-methionine = H(+) +
CC N(6)-methyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:60280, Rhea:RHEA-COMP:15542, Rhea:RHEA-COMP:15546,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:61929; EC=2.1.1.367;
CC Evidence={ECO:0000250|UniProtKB:Q5QD03};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00358,
CC ECO:0000269|PubMed:11691919}. Chromosome, centromere
CC {ECO:0000269|PubMed:11691919}. Note=Associates with centromeric
CC constitutive heterochromatin.
CC -!- TISSUE SPECIFICITY: Expressed in leaves stems and flowers.
CC {ECO:0000269|PubMed:11691919}.
CC -!- DOMAIN: Although the SET domain contains the active site of enzymatic
CC activity, both pre-SET and post-SET domains are required for
CC methyltransferase activity.
CC -!- DOMAIN: In the pre-SET domain, Cys residues bind 3 zinc ions that are
CC arranged in a triangular cluster; some of these Cys residues contribute
CC to the binding of two zinc ions within the cluster. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
CC superfamily. Histone-lysine methyltransferase family. Suvar3-9
CC subfamily. {ECO:0000255|PROSITE-ProRule:PRU00908}.
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DR EMBL; AF344446; AAK28968.1; -; mRNA.
DR EMBL; AC008017; AAD55657.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE35414.1; -; Genomic_DNA.
DR EMBL; AY099620; AAM20471.1; -; mRNA.
DR EMBL; BT002137; AAN72148.1; -; mRNA.
DR PIR; F96756; F96756.
DR RefSeq; NP_565056.1; NM_105968.3.
DR AlphaFoldDB; Q9C5P4; -.
DR SMR; Q9C5P4; -.
DR BioGRID; 28860; 10.
DR IntAct; Q9C5P4; 6.
DR STRING; 3702.AT1G73100.1; -.
DR PaxDb; Q9C5P4; -.
DR PRIDE; Q9C5P4; -.
DR ProteomicsDB; 226571; -.
DR EnsemblPlants; AT1G73100.1; AT1G73100.1; AT1G73100.
DR GeneID; 843641; -.
DR Gramene; AT1G73100.1; AT1G73100.1; AT1G73100.
DR KEGG; ath:AT1G73100; -.
DR Araport; AT1G73100; -.
DR TAIR; locus:2032592; AT1G73100.
DR eggNOG; KOG1082; Eukaryota.
DR HOGENOM; CLU_004556_2_1_1; -.
DR InParanoid; Q9C5P4; -.
DR OMA; VAIWKMS; -.
DR OrthoDB; 274915at2759; -.
DR PhylomeDB; Q9C5P4; -.
DR BRENDA; 2.1.1.367; 399.
DR PRO; PR:Q9C5P4; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9C5P4; baseline and differential.
DR Genevisible; Q9C5P4; AT.
DR GO; GO:0005694; C:chromosome; IDA:TAIR.
DR GO; GO:0000775; C:chromosome, centromeric region; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0003690; F:double-stranded DNA binding; IBA:GO_Central.
DR GO; GO:0010385; F:double-stranded methylated DNA binding; IDA:TAIR.
DR GO; GO:0042054; F:histone methyltransferase activity; ISS:TAIR.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0034968; P:histone lysine methylation; IEA:InterPro.
DR GO; GO:0040029; P:regulation of gene expression, epigenetic; TAS:TAIR.
DR Gene3D; 2.170.270.10; -; 1.
DR Gene3D; 2.30.280.10; -; 1.
DR InterPro; IPR025794; H3-K9-MeTrfase_plant.
DR InterPro; IPR003616; Post-SET_dom.
DR InterPro; IPR007728; Pre-SET_dom.
DR InterPro; IPR015947; PUA-like_sf.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
DR InterPro; IPR036987; SRA-YDG_sf.
DR InterPro; IPR003105; SRA_YDG.
DR Pfam; PF05033; Pre-SET; 1.
DR Pfam; PF02182; SAD_SRA; 1.
DR Pfam; PF00856; SET; 1.
DR SMART; SM00468; PreSET; 1.
DR SMART; SM00317; SET; 1.
DR SMART; SM00466; SRA; 1.
DR SUPFAM; SSF82199; SSF82199; 1.
DR SUPFAM; SSF88697; SSF88697; 1.
DR PROSITE; PS50868; POST_SET; 1.
DR PROSITE; PS50867; PRE_SET; 1.
DR PROSITE; PS51575; SAM_MT43_SUVAR39_2; 1.
DR PROSITE; PS50280; SET; 1.
DR PROSITE; PS51015; YDG; 1.
PE 2: Evidence at transcript level;
KW Centromere; Chromatin regulator; Chromosome; DNA-binding; Metal-binding;
KW Methyltransferase; Nucleus; Reference proteome; S-adenosyl-L-methionine;
KW Transferase; Zinc.
FT CHAIN 1..669
FT /note="Histone-lysine N-methyltransferase, H3 lysine-9
FT specific SUVH3"
FT /id="PRO_0000186074"
FT DOMAIN 208..355
FT /note="YDG"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00358"
FT DOMAIN 430..491
FT /note="Pre-SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00157"
FT DOMAIN 494..638
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT DOMAIN 653..669
FT /note="Post-SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00155"
FT DNA_BIND 108..120
FT /note="A.T hook"
FT REGION 56..127
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 270..290
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 56..112
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 432
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 432
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 434
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 438
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 438
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 445
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 447
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 473
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 473
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 477
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 479
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 483
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 504..506
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 540
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 542
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 592
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 595..596
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 598
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250"
FT BINDING 657
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250"
FT BINDING 659
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250"
FT BINDING 664
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="4"
FT /evidence="ECO:0000250"
FT CONFLICT 416
FT /note="S -> P (in Ref. 1; AAK28968)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 669 AA; 73439 MW; 8878E000747FD1AB CRC64;
MQGVPGFNTV PNPNHYDKSI VLDIKPLRSL KPVFPNGNQG PPFVGCPPFG PSSSEYSSFF
PFGAQQPTHD TPDLNQTQNT PIPSFVPPLR SYRTPTKTNG PSSSSGTKRG VGRPKGTTSV
KKKEKKTVAN EPNLDVQVVK KFSSDFDSGI SAAEREDGNA YLVSSVLMRF DAVRRRLSQV
EFTKSATSKA AGTLMSNGVR TNMKKRVGTV PGIEVGDIFF SRIEMCLVGL HMQTMAGIDY
IISKAGSDEE SLATSIVSSG RYEGEAQDPE SLIYSGQGGN ADKNRQASDQ KLERGNLALE
NSLRKGNGVR VVRGEEDAAS KTGKIYIYDG LYSISESWVE KGKSGCNTFK YKLVRQPGQP
PAFGFWKSVQ KWKEGLTTRP GLILPDLTSG AESKPVSLVN DVDEDKGPAY FTYTSSLKYS
ETFKLTQPVI GCSCSGSCSP GNHNCSCIRK NDGDLPYLNG VILVSRRPVI YECGPTCPCH
ASCKNRVIQT GLKSRLEVFK TRNRGWGLRS WDSLRAGSFI CEYAGEVKDN GNLRGNQEED
AYVFDTSRVF NSFKWNYEPE LVDEDPSTEV PEEFNLPSPL LISAKKFGNV ARFMNHSCSP
NVFWQPVIRE GNGESVIHIA FFAMRHIPPM AELTYDYGIS PTSEARDESL LHGQRTCLCG
SEQCRGSFG
